image/svg+xml
(Hernández & Gómez-Hinostrosa, 2015)
- Mammillaria
is distributed from the southern
United States to Central America.
- Mexico is the center of diversity for the genus
- The number of recognized species varies on
the author:
Reppenhagen (1992) considered 320 spp;
Pilbeam (1999) 181 spp and
Hunt (2006) 163 spp.
Its name derived from Latin mammilla, "nipple",
referring to tubercles.
https://github.com/cristoichkov/GBS_Bioinf_Process_Mamm
Changes circumscription of
M. haageana
according to some taxonomic
proposals.
Distribution of
M. haageana
M. haageana
subsp.
haageana M. haageana
subsp.
meissneri M. haageana
subsp.
meissneri M. haageana
subsp.
conspicua
M. haageana
subsp.
conspicua M. haageana
subsp.
conspicua M. haageana
subsp.
acultzingensis M. haageana
subsp.
san- angelensis
clust_threshold.
-This the level of sequence
similarity at which two sequences are
identified as being homologous, and thus
cluster together.
mindepth_majrul.
- This is the minimum depth
at which majority rule base calls are made
during step 5 consensus base calling.
Not recommend using values higher than 0.95, as homologous sequences may not cluster together at such high threshold due to the presence of Ns, indels, sequencing errors, or polymorphisms (Eaton, 2015).
++
Grupo
externo
Grupo
Interno
M. albilanata
ssp.
oaxacana
Mao_1
Mao_4
Mao_5
Mao_3
M. haageana
Mhsa
Mhm_1
Mhm_1
Mhm_3
Mhc_8
Mhc_7
Mhh_3
Mhc_5
Mhh_2
Mha_1
Mhh_1
Phylogenetic tree generated with
RAxML of 125 taxa based on two
chloroplast markers (rpl16 and
psbA-trnH), bootstrap support values
are shown. The concatenated matrix
follows a model of molecular evolution
TVM + I + G
Mammillaria zephyranthoides
Bravo-Hollis and Sánchez-
Mejorada (1991)
Pilbeam (1999) Reppenhagen (1992) Guzmán (2003) Hunt (2006)
M. haageana M. haageana M. haageana M. haageana M. haageana
M. vaupelii
ssp.
haageana M. meissneri
ssp.
haageana
M. collina
ssp.
conspicua M. donatii
ssp.
acultzingensis
M. donati
ssp.
elegans M. conspicua
ssp.
conspicua
M. san-angelensis
ssp.
san-angelensis
var.
vaupelii
ssp.
elegans
M. conspicua
ssp.
schmollii M. albidula
ssp.
meissneri
ssp.
acultzingensis M. elegans
ssp.
san-angelensis
var.
lupina
ssp.
vaupelii
var.
longicaudata
var.
teyuca
M. haageana
subsp.
san- angelensis
M. haageana
subsp.
acultzingensis
M. haageana
subsp. meissneri
M. haageana
subsp.
conspicua
M. haageana
subsp.
haageana
Escobaria_chihuahuensis
Pelecyphora_aselliformis
Coryphantha_pallida
Coryphantha_durangensis
Escobaria_zilziana
Coryphantha_hesteri
Coryphantha_vivipara
M_wrightii
M_barbata
M_luethyi
Neolloydia_conoidea
Ortegocactus_macdougallii
M_tetrancistra
M_guelzowiana
M_boolii
M_schumannii
M_pondii
M_halei
M_poselgeri
M_oteroi
M_zephyranthoides
M_beneckei
M_sphacelata
M_herrerae
M_humboldtii
M_candida
M_senilis
M_weingartiana
M_longimamma
M_moelleriana
M_hernandezii
M_pottsii
M_pectinifera
M_picta
M_prolifera
M_glassii
M_plumosa
M_bombycina
M_perezdelarosae
M_decipiens
M_elongata
M_microhelia
M_vetula_subsp_gracilis
M_melanocentra_subsp_rubrograndis
M_grusonii
M_mammillaris
M_magnimamma
M_lindsayi
M_peninsularis
M_rhodantha
M_huitzilopochtlii_ssp_huitzilopochtlii
M_huitzilopochtlii_ssp_niduliformis
M_crucigera_tlalocii
M_crucigera_ssp_crucigera
M_albilanata_ssp_oaxacana_CC036
M_lanata
M_eriacantha
M_columbiana_ssp_columbiana
M_columbiana_ssp_yucatanensis
M_albilanata_ssp_oaxacana_CC044
M_haageana_CC024
M_haageana_CDMX
M_albilanata_ssp_oaxacana_CC046
M_haageana_CC023
M_haageana_CC025
M_haageana_CC027
M_dixanthocentron
M_supertextae
M_haageana_CC045
M_albilanata_ssp_reppenhagenii
M_albilanata_ssp_tegelbergiana
M_albilanata_ssp_albilanata
M_haageana_CC039
M_albilanata_ssp_oaxacana_CC040
M_favicentra
M_haageana_CC022
M_haageana_CC035
M_haageana_CC021
M_haageana_CC029
M_haageana_CC020
Ser.
Polyacanthae
Ser.
Leucocephalae
Ser.
Polyedrae
Ser.
Lasiacanthae
subg.
Chilita
Outgroup
100
22
28
58
87
82
100
100
99
52
93
76
89
94
90
44
59
42
98
58
83
90
33
52
60
52
53
4
17
14
34
43
100
100
72
42
54
83
37
24
11
92
39
67
87
91
79
83
40
54
65
36
23
65
87
30
41
27
clade S1
clade S2
clade S3
clade S4
Morphological variation in
M. haageana
Phylogenetic analysis
to know the position of
M. haageana
Selected samples and plate design for sequencing using GBS
Bioinformatic workflow
97.2%
2.79%
94.74%
5.25%
95.41%
4.58%
0
25
50
75
100
GBSXipyradStacks
Demultiplex software
Percentage %
No_match_reads
Match_reads
6e+06
4e+06
2e+06
1e+06
8e+05
Samples
Number of reads
Species
M_albilanata_albilanta
M_albilanata_oaxacana
M_albilanata_reppenhagenii
M_crucigera
M_dixanthocentron
M_duoformis
M_flavicentra
M_haageana_acultzingensis
M_haageana_conspicua
M_haageana_haageana
M_haageana_meissneri
M_haageana_san_angelensis
M_huitzilopochtli
M_lanata
M_magnimamma
M_myxtax
M_supertexta
20000
40000
60000
0.820.850.880.910.94
Clust threshold
Number of SNPs
min_sam_loc
40%
60%
80%
1000
2000
3000
4000
0.820.850.880.910.94
Clust threshold
Number of loci
min_sam_loc
40%
60%
80%
25000
50000
75000
100000
3456
Mindepth majrule
Number of SNPs
min_sam_loc
40%
60%
80%
1000
2000
3000
4000
3456
Mindepth majrule
Number of loci
min_sam_loc
40%
60%
80%
−75
−50
−25
0
25
0.82/0.850.85/0.880.88/0.910.91/0.94
Iteration of clust threshold
Number of new Loci
DGDC-REPSA-PAPIME-PAPIIT
Acknowledgment
Comparison between three software
Number of reads per sample
Plots of iterating values of the level of sequence similarity
Plots of iterating values the minimum depth
Plots of the number of new loci
Not recommend using values higher than 0.95, as homologous sequences may not cluster together at such high threshold due to the presence of Ns, indels, sequencing errors, or polymorphisms (Eaton, 2015).
++
This Figure describes how increasing values for clust_threshold
contributed new broadly shared, and therefore likely real loci.
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